Nextflow workflow report

[big_planck]

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 125.

The full error message was:

Error executing process > 'NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9626017_SRR13191702)'

Caused by:
  Process `NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9626017_SRR13191702)` terminated with an error exit status (125)


Command executed:

  wget \
      -t 5 -nv -c -T 60 \
      -O SRX9626017_SRR13191702_1.fastq.gz \
      ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz
  
  echo "89c5be920021a035084d8aeb74f32df7  SRX9626017_SRR13191702_1.fastq.gz" > SRX9626017_SRR13191702_1.fastq.gz.md5
  md5sum -c SRX9626017_SRR13191702_1.fastq.gz.md5
  
  wget \
      -t 5 -nv -c -T 60 \
      -O SRX9626017_SRR13191702_2.fastq.gz \
      ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz
  
  echo "56271be38a80db78ef3bdfc5d9909b98  SRX9626017_SRR13191702_2.fastq.gz" > SRX9626017_SRR13191702_2.fastq.gz.md5
  md5sum -c SRX9626017_SRR13191702_2.fastq.gz.md5
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP":
      wget: $(echo $(wget --version | head -n 1 | sed 's/^GNU Wget //; s/ .*$//'))
  END_VERSIONS

Command exit status:
  125

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/wget:1.20.1' locally
  1.20.1: Pulling from biocontainers/wget
  docker: [DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of quay.io/biocontainers/wget:1.20.1 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/.
  See 'docker run --help'.

Work dir:
  /workspace/fetchngs/work/d9/d9fbfbff13acf3576969ba7b0629e2

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Run times
06-Jun-2024 12:34:53 - 06-Jun-2024 12:35:18 (duration: 25.1s)
  12 succeeded  
  0 cached  
  0 ignored  
  10 failed  
Nextflow command
nextflow run nf-core/fetchngs -profile docker --input ids.csv --outdir output
CPU-Hours
(a few seconds)
Launch directory
/workspace/fetchngs
Work directory
/workspace/fetchngs/work
Project directory
/home/gitpod/.nextflow/assets/nf-core/fetchngs
Script name
main.nf
Script ID
0f0b67958c4853dabf8556e682b6a379
Workflow session
37d2f9b2-eb2f-495e-a8fc-cee134bae64a
Workflow repository
https://github.com/nf-core/fetchngs, revision master (commit hash 8ec2d934f9301c818d961b1e4fdf7fc79610bdc5)
Workflow profile
docker
Nextflow version
version 24.04.2, build 5914 (29-05-2024 06:19 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.

(tasks table omitted because the dataset is too big)